segment cells in Dapi image
doCellSegmentation(
raster_img,
folder_path,
reduce_resolution = 4,
overlapping_pixels = 50,
python_path = NULL
)raster image; Dapi image of cells
character; where to save the file
numeric; the original Dapi image from Vizgen works better in the Mesmer algorithm if its resolution is reduced 4 times.
numeric; the number of pixels to overlap when calculating the rolling window
specify specific path to python if required
segmentation results
This function is a wrapper for the Mesmer algorithm implemented in python. It segments the cells in tissue by applying a rolling window on the complete image. It saves all the files in the specified folder with the coordinates of the tile: sx (start x), ex (end x), sy, and ey.